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PDB Id
Uniprot Id
Source Organism
Host Organism
Protein Name
Method
Summary
Structure Feature
Experiment
Ligands & Environment
7ZPJ
pdb_00007zpj
10.2210/pdb7zpj/pdb
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FASTA
PDB
MMCIF
Binary MMCIF
XML
Structure Factors
Full Validation Report
Validation File (XML)
Validation File (CIF)
FASTA Zipped(.gz)
PDB Zipped(.gz)
MMCIF Zipped(.gz)
Binary MMCIF Zipped(.gz)
Structure Factors Zipped(.gz)
Validation File Zipped (.xml.gz)
Validation File Zipped (.cif.gz)
ELECTRON MICROSCOPY
Sample
Pre-dicing state of mouse somatic dicer with pre-mir-15a and TARBP2
Specimen Preperation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Described in STAR methods
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
437518
Reported Resolution (Å)
3.81
Resolution Method
FSC 0.143 CUT-OFF
Other Details
?
Refinement Type
Symmetry Type
POINT
Map-Model Fitting and Refinement
ID
1
Refinement Space
REAL
Refinement Protocol
FLEXIBLE FIT
Refinement Target
Ramachandran Plot, Rotamer Analysis, Density Fit Analysis, Correlation coefficient
Overall B Value
189.2
Fitting Procedure
?
Details
We used our previous deposition 7YYM as an initial model source. TARBP2 initial coordinates were predicted by AlphaFold. Initial local fitting was done using Chimera and then Coot's Real Space Refine Zone. PHENIX Real-space refinement was used for flexible fitting. ISOLDE was used for flexible fitting with torsion restraints defined for polypeptide chain and distance restraints for polyribonucleotides.
Data Acquisition
Detector Type
GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å
2
)
60.198
Imaging Experiment
Date of Experiment
?
Temprature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
800
Maximum Defocus (nm)
3500
Minimum Tilt Angle (degrees)
?
Maximum Tilt Angle (degrees)
?
Nominal CS
?
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
?
Nominal Magnification
?
Calibrated Magnification
?
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
?
Imaging Experiment
Task
Software Package
Version
PARTICLE SELECTION
Topaz
?
CTF CORRECTION
cryoSPARC
v3.3.1
MODEL FITTING
UCSF Chimera
1.15
CLASSIFICATION
cryoSPARC
v3.3.1
RECONSTRUCTION
cryoSPARC
v3.3.1
MODEL REFINEMENT
Coot
0.9.6
MODEL REFINEMENT
PHENIX
1.19.2-4158
MODEL REFINEMENT
ISOLDE
1.1.0
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
?
